HsaINT0095633 @ hg19
Intron Retention
Gene
ENSG00000198670 | LPA
Description
lipoprotein, Lp(a) [Source:HGNC Symbol;Acc:6667]
Coordinates
chr6:160952515-160953681:-
Coord C1 exon
chr6:160953563-160953681
Coord A exon
chr6:160952923-160953562
Coord C2 exon
chr6:160952515-160952922
Length
640 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTCCCCTACCTCTGTTTAGGGT
3' ss Score
10.27
Exon sequences
Seq C1 exon
GTACCTTTGGGACTGGCCTTCTCAAGGAAGCCCAGCTCCTTGTTATTGAGAATGAAGTGTGCAATCACTATAAGTATATTTGTGCTGAGCATTTGGCCAGAGGCACTGACAGTTGCCAG
Seq A exon
GTAAGAAAAGATCAATAGATCAAAGTCTTGTGCTCTCCCGTCTCAGTCTCAGTCCCTTAGACGTCAGTCCCAAAGTGGCAAATTCAGGAAGGTTTTGTCAGTGGAAGACCCCAGTCTAAGTGTTGCTCAGAAACTCCCCAGATCTGTCCCTGAATGCATATTCAGATCATCTAAGGAGACGTCTTGGGGCTTGAGTTCCAGATCCATAGCAAGGGAGCCGTAAGTGCCATAACTACCTCAGGCCACTCACCTTCCTGGTGTGTGCTGGTCACCAGTGACTGAAGTGGTGGCTTTTCCAGTAGAGAGGAAGGTAGAGGGTACAGGACCGAGACAAATTACACACACTTAACAATGATGTCCAGGCTAGCCCAGTCTAAAGGAAACACCAAGTTAGGAAGCAATGCATGCAGGATTCACAAGGGATTATTTTTTTTCCCAGGAAAAAACTAAGTGATGTGGTTTTGTTGAATAGACTTTGCTAAGTACTTAAGCACTGCAGATGCTTGAGTAATATGCTCATAAGTTCCTTTCTGATTTGAATTACTGGGAAAATGTACATATGGATAAGAGAAGGATGGCATCCCATATTAAAAGGTTGGCAGCTTAAAGCTCACATGAATTTTCCCCTACCTCTGTTTAG
Seq C2 exon
GGTGACAGTGGAGGGCCTCTGGTTTGCTTCGAGAAGGACAAATACATTTTACAAGGAGTCACTTCTTGGGGTCTTGGCTGTGCACGCCCCAATAAGCCTGGTGTCTATGCTCGTGTTTCAAGGTTTGTTACTTGGATTGAGGGAATGATGAGAAATAATTAATTGGACGGGAGACAGAGTGAAGCATCAACCTACTTAGAAGCTGAAACGTGGGTAAGGATTTAGCATGCTGGAAATAATAGACAGCAATCAAACGAAGACACTGTTCCCAGCTACCAGCTATGCCAAACCTTGGCATTTTTGGTATTTTTGTGTATAAGCTTTTAAGGTCTGACTGACAAATTCTGTATTAAGGTGTCATAGCTATGACATTTGTTAAAAATAAACTCTGCACTTATTTTGATTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198670-LPA:NM_005577:39
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(18.2=100)
A:
NA
C2:
PF0008921=Trypsin=PD(21.0=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACCTTTGGGACTGGCCTTCT
R:
AGCATGCTAAATCCTTACCCACG
Band lengths:
349-989
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)